calculate loGP with cxcalc for structures with salts
I calculate logp with command line cxcalc.
I'm asking if when i have a structure with two ions : a small and a big ions,
the logp calculation of this structure remove the small ion and take into account only the big ion.
If you want logP of ionic form of a submitted molecule then you need to use the "-t logPMicro" option
cxcalc logP "your molecule" -t logPMicro
The dafault setting of logP calculator will neutralize the submitted molecule if possible.
In the case of simple acidic/basic molecules the neutralization is clear. It means adding or removing a hydrogen (as if pH would be changed) if the submitted acidic/basic center is ionized.
In the case of zwitter ions ,however, the logD is calculated at the isoelectric point.
With the default logP setting you always calculate the "neutral" logP
cxcalc logP "your molecule"
You can calculate both "ionic" and "neutral" logP with this command.
cxcalc logP "your molecule" -t logPMicro, logPTrue
Do you want to remove the counterion of a salt?
e.g. Cation(+) Cl(-) , here Cl(-) is the small counterion.
In this case you need use the standardizer.
yes i use the standardizer :
standardize molfile -c "keepone" -f mol| cxcalc -N - hi logp -p 3
But i obtain the same result when i use only cxcalc -N - hi molfile logp -p 3
i obtain the logp of the non ionic species when i have :
Cation(+) Cl(-) , here Cl(-) is the small counterion.
is it normal?
It seems that the default setting of the logP's standardizer in cxcalc removes the smallest counterion. This is why you obtained the same result.
May be it is not normal that the default logP's setting do this.
I ask somebody for checking logP's standardizer.
We discussed this problem. And the conclusion is that this is the normal behaviour of the logP calculation in cxcalc.
Ok thank you .